Experimental Design and Controls


Experimental Design Questions

Define probe v. target
Label RNA v. cDNA (impact on spotted material)
Cy series v. Alexa series dyes
Spots made of oligos v. cDNA
Affymetric chips v. printed glass chips
Reproducibility within and between labs

Controls

Dye reversal
Pooled v. control reference mRNA
Control spots from another species

Our Research

How do you know if what you are measuring accurately represents your sample?

Layout of our DNA Microarray

 


Calibrated Acquisition of Fluorescence

 

Tested Concentration of Spotted Materials (4,102 fold range)

 

Unexpected Gene-specific Variation

 

Compared Three Detection Variations

 


 

Wanted to Improve Quality of Signal: Clone PCR Products

Original PCR Products
Cloned PCR Products

 

Optimized Experimental Conditions: Signal Up and Noise Down

 

What about Other Ratios? 10:1, 3:1, 1:1, 1:3, 1:10


Good Trends


CSU Workshop

Genomics Course Page

Biology Department Main Page


Send comments, questions, and suggestions to: macampbell@davidson.edu or (704) 894 - 2692
© Copyright 2003 Department of Biology, Davidson College, Davidson, NC 28035